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Our future, our universe, and other weighty topics

Friday, January 3, 2014

The Origin of Life: Programmatically Predestined?

Let us now look
at one of the great mysteries of the universe, the mystery of the
origin of life, something that took place more than three billion
years ago.

Some readers may
be thinking along these lines: That's not such a mystery. Given a
primordial soup and millions of years of time, there developed some
self-replicating molecule. Once you had that, the development of
everything else was just a case of things evolving from the simple to
the more complex.

But such a glib
explanation glosses over the great difficulties involved in
explaining the origin of life on the early Earth. The fact is that
there are huge difficulties in explaining how life began on our
planet billions of years ago. In recent decades scientists have
made relatively little progress in solving this problem.

Consider the
progress of astronomy during the past 50 years. Since the year 1963
we have seen the discovery of the Big Bang, the discovery that the
expansion of the universe is accelerating, and the discovery of more
than 1000 extrasolar planets. But without doing a Google search, can
you name one bit of progress that has been made in the past 50 years
regarding the origin of life? You probably can't. When most of us
think of scientific work on the origin of life, we think back to the
Miller experiments involving amino acids, but they were done in the
1950's.

We can divide up
the problem of the origin of life into three different problems: a
necessary components problem, a combinatorial problem, and a
computation problem.

The Necessary
Components Problem

The basic units
of life (below the cellular level) are things such as RNA, DNA, and
proteins. Proteins are made of building blocks called amino acids.
Some proteins are extremely complicated molecules built from very many
amino acids. It was calculated long ago that the chance of some of
these proteins forming from random combinations of amino acids is
incredibly low, even given billions of years. But that's not
necessarily a problem, because proteins are formed using the
instructions in DNA. A DNA molecule is like a library of recipe
books, with each of the recipes being a recipe for making a
particular type of protein.

So if there is a
mechanism for producing DNA from a chance combination of chemicals,
we might have a way of explaining how all those complicated proteins
came into existence. Unfortunately it seems DNA molecules appear to
be way too complicated to have arisen from a chance combination of
their constituent elements of nucleotides (which consist of sugars,
phosphates, and nitrogenous bases), without assistance from something more complicated than nucleotides.

So the current
leading hypothesis is that the first self-replicating molecule was
not DNA but something simpler, presumably some version of RNA. This
idea is called the RNA World hypothesis. The idea is that first
there was RNA, and that DNA evolved later. However, the
RNA World hypothesis is on shaky ground.

One problem is
the difficulty of explaining the origin of all the necessary building
blocks. The table below
shows the various types of building blocks. As indicated below,
there are reasons for doubting that the ribose sugars, purines, and
nucleotides would have existed in sufficient quantity for DNA or RNA
to originate.

Components

RNA, DNA

Ribose
sugars

Harvard
science web site: "In experiments ribose could not be made
at the necessary quantities that would explain its abundance on
early Earth because it was highly unstable."

Wikipedia article:
some scientists have concluded that "the backbone of the
first genetic material could not have contained ribose or other
sugars because of their instability."

Phosphates

Pyrimidines
(type of nitrogenous base)

2009 paper
(Powner et. al) suggests possible path for abiotic origin.

Purines
(type of nitrogenous base)

More
complex than pyrimidines. According to this paper, hard to explain abiotic origin, in a
way compatible with formation of ribose sugars.

Nucleosides
(combination of ribose sugar and pyrimidines or purines) and nucleotides (a nucleoside plus a phosphate)

Wikipedia article: “No known
chemical pathways for the abiogenic synthesis of nucleotides
from pyrimidine nucleobases cytosine and uracil under prebiotic
conditions."

Proteins

Amino Acids

Found in a
meteorite. Miller-Urey experiment produced amino acids from
gases and continuous electricity.

The
Combinatorial Problem

The combinatorial
problem is the problem of getting anything like RNA or DNA to appear
from the building blocks listed above. This scientific paper by Joyce and Orgel refers to the difficulty of
joining together nucleosides (a combination of ribose sugar and
pyrimidines or purines) and nucleotides (a nucleoside plus a
phosphate). The wikipedia article on the RNA World hypothesis notes
that “Joyce and Orgel further argued that nucleotides cannot link
unless there is some activation of the phosphate group, whereas the
only effective activating groups for this are 'totally implausible in
any prebiotic scenario', particularly adenosine triphosphate.”

Well-known
scientist Freeman Dyson has stated, “The results of thirty years of
intensive chemical experimentation has shown that prebiotic synthesis
of amino acids is easy to simulate in a reducing environment, but
prebiotic synthesis of nucleotides is difficult in all
environments...If it happened, it happened by some process that none
of our chemists have been clever enough to reproduce.”

RNA is made of
nucleotides, which are made of ribose sugar, phosphates, pyrimidines,
and purines. Scientists have not been able to synthesize RNA through
a simulation of the early earth, and in such simulations have not been able to make the
simpler nucleotides either. As discussed in the table above, there
are difficulties in assuming the availability of even some of the
building blocks of the building blocks of RNA.

The
Computational Problem

Perhaps the
biggest problem involving the origin of life is the problem of accounting
for the origin of the genetic code. The genetic code is a symbolic
representation system used by all earthly life. It has been called a
kind of miniature programming language.

The Genetic Code

It is fairly easy
to explain the basics of how the code works. In the spiral staircase
structure of the DNA molecule, the “steps” of the staircase are
chemicals called nitrogenous bases: either purines (adenine or guanine) or
pyrimidines (cytosine or uracil). Various combinations of three of
these chemicals stand for different amino acids (the building blocks
of proteins). For example, if there are three consecutive “steps”
in the spiral staircase, and the first is cytosine, the second
adenine, and the third guanine, that stands for the amino acid
glutamine. There are 63 other cases where a sequence of three
nitrogenous bases stands for a particular amino acid. (In the diagram above, the chemicals around the four edges of the square are the amino acids.)

Imagine if you
liked to write down recipes, but you needed to write down many of
them on a single piece of paper. You might invent a little “recipe
language” in which MK1 stands for a half a cup of milk, MK2 stands
for a full cup of milk, FL1 stands for a half a cup of flour, and so
forth, with a total of 64 different three-character symbols (and some
other characters standing for “end of recipe”). You might then
write out recipes very concisely using this little language. That's
quite similar to what the genetic code does, except the recipes are
stored in the DNA molecule, and the recipes are instructions for
making proteins from the building blocks of amino acids.

The big question
is: how did this genetic code ever originate? It's hard to imagine it
arising through anything like Darwinian evolution, as the genetic
code seems to be required from the very beginning of biological
evolution.

The genetic code
can be considered an example of code, the term software
developers use for the symbolic instructions they create. The
baffling question is: how did nature go from chemicals to code? Code seems like
something fundamentally different from chemicals, and the two seem as
unrelated as an apple is to a bicycle.

The issue was
highlighted by a paper by biologists J.T. Trevors and D.L. Abel:"Peer-reviewed life-origin literature presupposes that, given enough time, genetic instructions arose via natural events. Thus far, no paper has provided a plausible mechanism for natural-process algorithm-writing...There is an immense gap from prebiotic chemistry and the lifeless Earth to a complex DNA instruction set, code encryption into codonic sequences, and decryption (translation) into amino acid sequences...How did inanimate nature write(1) the conceptual instructions needed to organizemetabolism?(2) a language/operating system needed to symbolicallyrepresent, record and replicate those instructions?(3) a bijective coding scheme (a one-to-one correspondenceof symbol meaning) with planned redundancyso as to reduce noise pollution between triplet codon‘‘block code’’ symbols (‘‘bytes’’) and amino acidsymbols?We could even add a fourth question. How didinanimate nature design and engineer(4) a cell [Turing machine? (Turing, 1936)] capable ofimplementing those coded instructions?" -- Trevors and Abel

In
this article the widely read physics professor Paul Davies has
discussed other difficulties in the “code from chemicals”
scenario, the assumption that the genetic code arose from some kind
of chemical evolution:

"The
language of genes is digital, consisting of discrete bits, cast in
the language of a four-letter alphabet. By contrast, chemical
processes are continuous. Continuous variables can also process
information – so-called analogue computers work that way – but
less reliably than digital. Whatever chemical system spawned life, it
had to feature a transition from analogue to digital. The way
life manages information involves a logical structure that differs
fundamentally from mere complex chemistry. Therefore chemistry alone
will not explain life's origin, any more than a study of silicon,
copper and plastic will explain how a computer can execute a program." -- Davies

This problem of the origin of the genetic code recently got even more difficult to explain, because scientists recently announced the discovery of a second genetic code buried in DNA. Apparently many of the triple sequences have a double-meaning. Explaining one genetic code was a nightmare -- how can we explain two of them?

A New Approach
to the Origin of Life

We
might get around these difficulties by imagining that the origin of
life on Earth required external intervention by a divine agent or
perhaps extraterrestrials. But that would raise the question: why
should our ordinary little rock have deserved such a special
blessing? After all, modern astronomy tells us that planets are as
common as apples in an apple orchard.

A
more intellectually attractive idea is the daring concept that the origin of
life was programmatically predestined. We can boldly postulate that long,
long before there arose the programming in the genetic code, there
was a more general programming woven into the fabric of the universe,
a programming that drives the evolution of the universe, causing the
frequent occurrence of things that might otherwise have very little or no chance of
occurring. Under such a scenario, we can think that life is
appearing throughout the universe, because that is the way the
universe is programmed to behave. Under such a concept, we no longer
have to imagine the origin of the genetic code by supposing a farfetched case of
“code from chemicals.” We can instead plausibly imagine the origin of the genetic code
as a case of “code from code” – the genetic code being a
product of a more general cosmic software that is influencing cosmic
destiny, propelling the universe forward towards desirable outcomes.

There
are actually many reasons for adopting such a theory, and most of
them come not from the world of biology, but from the worlds of
physics and cosmology. I will be presenting some of these reasons in
a lengthy blog post I will post on this blog on Sunday, January 5th.

Copyright Notice

All posts on this blog are authored by Mark Mahin, and are protected by copyright. Copyright 2013-2014 by Mark Mahin. All rights reserved. Any resemblance between any fictional character and any real person is purely coincidental.